The war brought Weyoun into contact with many leaders from the Alpha Quadrant. He visited Deep Space 9 to negotiate with Benjamin Sisko when the cold war between the powers of the Alpha Quadrant and the Dominion showed signs of eroding into open hostilities. Shortly thereafter, he returned with a fleet of Cardassian and Dominion warships to take control of the station, and went on to serve as the Dominion overseer of the station during the brief occupation that followed. In this capacity, he personally negotiated a nonaggression pact with Bajor and dealt with representatives from such powers as the Romulan Star Empire, Breen Confederacy, and Tholian Assembly. Until his death, he remained the only "Solid" that the Female Changeling claimed that she had ever trusted.

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Weyoun 4 was encountered by the Federation in 2372 as the supervisor of a Jem'Hadar attack ship and its crew of Jem'Hadar, led by Omet'iklan. After his ship was attacked by a group of renegade Jem'Hadar, Weyoun chose to recruit the assistance of Captain Sisko in quelling the rebellion. Weyoun withheld crucial information from Omet'iklan about the rebels' fortress: an Iconian gateway on Vandros IV. However, the Jem'Hadar under Weyoun's supervision remained loyal to the Founders and successfully completed the mission of eradicating the Jem'Hadar rebellion. Following the battle, Omet'iklan killed Weyoun for questioning his loyalty to the Dominion. (DS9: "To the Death")

According to the script for "To the Death", when Weyoun slaps Odo on the shoulder, he infected him with the virus that presents itself in "Broken Link" and necessitates his return to the Great Link. [1]

In 2373, the next clone, Weyoun 5, was assigned as liaison and adviser to Gul Dukat, the dictator of the newly Dominion-annexedCardassian Union. Although there were frequent disagreements concerning overall policy, Weyoun believed that he had developed a good working relationship with Dukat in the short time they had worked together. (DS9: "Ties of Blood and Water", "Call to Arms")

Just prior to the beginning of the Dominion War, Weyoun issued an ultimatum to Captain Sisko, demanding that the Federation remove the minefield they had started laying at the mouth of the Bajoran wormhole. Sisko refused, and Weyoun, along with Dukat, led an assault fleet to capture the station by force. (DS9: "Call to Arms")

In 2374, during the Dominion occupation of DS9, then known again as Terok Nor, Weyoun and Dukat formed the Ruling Council to manage station affairs. Weyoun offered Odo, whom he still revered as one of the Founders, a position on the Council, which Odo eventually accepted. When the Female Changeling arrived on the station a few months later, Weyoun observed that she had done a good job "neutralizing" Odo as a threat, not realizing the Founders' interest in Odo was for his own sake. (DS9: "A Time to Stand", "Favor the Bold")

Despite his race's lack of a sense of aesthetics, he attempted to learn to appreciate Tora Ziyal's artwork. He asked Kira Nerys for help with this, but she was dismissive. (DS9: "Favor the Bold")

Weyoun returned to Cardassia Prime following the recapture of DS9 by the Federation. Because of Gul Dukat's failure and descent into madness, Weyoun appointed Damar to be the new leader of the Cardassian Union. Over the next few months, he took a more forceful approach with Damar, ordering him to initiate peace talks with the Federation in order to arrange the acquisition of the Kabrel system without the Federation's knowledge of its significance. However, the plan failed when the Federation determined why the Dominion wanted Kabrel: to harvest tri-nucleic fungi that could be used to manufacture ketracel-white for the Jem'Hadar. (DS9: "Statistical Probabilities")

A group of genetically-engineered Humans used a holographic recording of Weyoun to help uncover a move by the Dominion to acquire a strategic planet in the Kabrel system that would have allowed them to produce ketracel-white.(DS9: "Statistical Probabilities")

The next clone, Weyoun 6, was activated shortly after Weyoun 5's demise. This new clone proved to be "defective," in that he strongly felt that the Dominion's war against the Alpha Quadrant was a mistake. However, he still maintained his loyalty to the Founders, and therefore contacted Odo, under the guise of GulRussol, and requested a meeting, so he could announce his intentions to defect to the Federation. Aboard the runaboutUSS Rio Grandeen route back to DS9, Weyoun 6 explained to Odo not only how he wanted to prevent further conflict, but also how the Great Link had been afflicted by a wasting disease that was slowly killing all Founders, except for Odo. When the runabout was located by his replacement, Weyoun 6 activated his termination implant so Weyoun 7 would call off his attacks, thus saving Odo. The "defective" clone died in peace, with a blessing from one of his gods. (DS9: "Treachery, Faith and the Great River")

When Weyoun 7 was activated, he ordered a massive search to prevent Weyoun 6 from defecting to the Federation. Weyoun 7 was contacted by his predecessor so he could witness Weyoun 6 voluntarily activate his termination implant, thus removing the reason the Jem'Hadar were attacking Odo's runabout. Once this was done, Weyoun 7 called off the attack and wished Odo "a safe and pleasant journey back to DS9." (DS9: "Treachery, Faith and the Great River")

By late 2375, Weyoun 7 was in charge of a massive research project to find a cure for the Founders' disease. He also supported the Female Changeling in her negotiations to arrange the alliance between the Dominion and the Breen Confederacy. While attending to the transfer of captured Starfleet officers Worf and Ezri Dax from a Breen starship to Dominion custody, he mentioned that he wished them to be held in a cell together due to his desire to see them "comfort each other" sexually. During a later meeting with the captured Worf and Ezri Dax, he tried to goad Ezri into cooperating with a further interrogation by referencing her feelings for Bashir -- to which Worf responded by abruptly breaking his neck, killing Weyoun 7 instantly. Damar, who was escorting Weyoun, reacted only by stopping his guards from taking action against Worf and then bursting into laughter, amused by both the meaninglessness of killing a Weyoun (as another clone would quickly take his place) and that Worf missed the opportunity to kill him, a far more valuable target. To Weyoun's fatal arrogance towards Worf, he explained simply to a befuddled Worf and Ezri Dax, "Overconfidence: the hallmark of the Weyouns. Maybe the Founders should eliminate you from their genetic recipe next time! (To Worf:) I'll just make another copy of him, you know. You should have killed me. There's only one Damar." (DS9: "Strange Bedfellows")

Weyoun 8 was activated shortly thereafter, and continued to oversee the war effort for the Dominion. He was initially unaware, however, that Damar had decided to turn against the Dominion and had arranged for Worf and Ezri to escape. Soon after, Damar publicly denounced the Dominion alliance and announced the first strike by the newly-formed Cardassian Liberation Front against the Dominion's primary cloning facility on Rondac III With no means to clone Weyoun again until those facilities were rebuilt, Weyoun 8 was possibly the last of the Weyouns. He immediately concluded that was precisely the reason Damar had chosen Rondac as a target. (DS9: "The Changing Face of Evil")

Weyoun would ensure that Damar and his supported paid dearly for this attack. Acting on the Female Changeling's orders, Weyoun had Dominion forces hunt down and execute Damar's wife and children. (DS9: "Tacking Into the Wind") Despite some initial victories, under the guidance of Kira Nerys, Weyoun's forces successfully waged a devastating counter-strike against the resistance, successfully destroying all eighteen rebel bases, as well as wiping out the sympathetic forces of Legate Goris and Gul Seltan with the help of collaborator Gul Revok. Having assumed Damar to have died in the attack, Weyoun publicly announced the defeat of the rebellion and the death of Damar. Much of the civilian population, however, having become disillusioned with Dominion rule themselves, were skeptical of Weyoun's claims. Indeed, Damar reemerged shortly thereafter and began rallying the people against the Dominion. (DS9: "Tacking Into the Wind")

After Damar's followers successfully sabotaged the planet's power systems, causing a planet-wide blackout, Weyoun proposed retaliation against the Cardassian population themselves, with the Female Changeling's approval. Weyoun then ordered the destruction of Lakarian City and its entire inhabitants of two million people, announcing its destruction on a planet-wide broadcast. Rather than forcing the Cardassians into submission, this act only motivated Damar to lead his remaining forces in an attack on Dominion Headquarters, as well as causing the Cardassian fleet, then engaging the Federation Alliance forces in the Battle of Cardassia, to switch sides against the Jem'Hadar and Breen fleets.

Enraged by this betrayal the Female Changeling ordered Weyoun to begin exterminating the entire Cardassian population. This act of genocide would lead to the death of over eight hundred million Cardassians before it was halted.

With the Jem'Hadar and Breen forces having been driven back to Cardassia Prime, Dominion Headquarters was stormed by Damar's forces. Though Damar himself was killed in the assault, Elim Garak, Kira, and Ekoor reached the main control room, capturing the Female Changeling. When Weyoun, upon hearing of Damar's death, mocked him and the devastation of Cardassia, prompting Garak to shoot and kill Weyoun. After the clone died, the Female Changeling mourned him thusly to Garak, who had fired the fatal shot: "I wish you hadn't done that. That was Weyoun's last clone." Garak sardonically replied "I was hoping you'd say that."
(DS9: "What You Leave Behind")

The role of Weyoun was created specifically for actor Jeffrey Combs by Ira Steven Behr and Hans Beimler, as Combs' previous appearances on Star Trek: Deep Space Nine had been in two roles - Tiron and Brunt - for which his face had been covered by heavy prosthetic make-up. (Star Trek: The Magazine Volume 1, Issue 17, p. 16) Combs has said that Weyoun is his personal favorite out of all the Star Trek roles he has played, due to his relatively increased input on the role. [2] The actor has also commented about Weyoun, "I love about him his grace and poise and ruthlessness and loyalty. Something that I really wanted to instill in him was, you know, you kinda have to fly by the seat of your pants. I really didn't know what he looked like, I didn't know anything about the design concept of the character when I arrived that first morning. I'd had a script for a couple of days, but I tend to really get a lot of hints from the outside, that tells me who I am inside. It does with all of us, the kind of shoes you wear tells you who you are. So when the process started, I began to see how sort of royal and regal he was, and there was something kind of Japanese, but also he was the courtier in the court, he was the foppish, coiffed, graceful diplomat who would go from one party to another and make them all run smoothly. And he would do anything he could, with a smile, to make it look as easy as possible, and get exactly what he wanted. So I took a little spice from the French court as well." (Hidden File 02, DS9 Season 7 DVD special features)

On another occasion, Combs elaborated, "I didn't think of Weyoun as evil, I think that's a mistake; it's always best to play them as if everything they do is justified. I played him as if he prided himself on how eloquent and elegant he could be, and on his ability to manipulate and cajole. He considered himself really adept at the political game. Sometimes I think he felt misunderstood, but he was a good actor too, feigning shock or surprise. Pretending you're vulnerable and that you're genuinely taken aback by someone's harsh words can be a useful tool, making the other person think that you're off balance when really you're two or three steps ahead." (Star Trek: The Magazine Volume 1, Issue 17, pp. 17-18)

"Ties of Blood and Water" reintroduced Weyoun after his "death" in "To the Death" and reveals that the Vorta clone themselves (a premise which was created specifically so Jeffrey Combs could reprise the role). As Ira Steven Behr explained, "When we first saw Jeff Combs do the role in 'To the Death,' we were wishing we could find a different ending to the episode, because we really didn't want the character to die. But we couldn't think of anything. The next thing you know, they're out in Griffith Park, shooting the fight, and he's dead. I knew immediately that he had to come back. There was no way he couldn't." (Star Trek: Deep Space Nine Companion, p. 442) Combs added in this respect, "I think that came from the fact that the very first time I played Weyoun he was killed, and that they realized that they liked the character! Necessity is the mother of invention, so they decided that the best thing to justify bringing him back was that he could be cloned. Then I think they saw the dramatic value of it, and the joke that he's constantly dying but he comes right back, even in the same episode. In the end they destroy the cloning facilities, but if you don't think that the Vorta are clever enough to not put all their cloning eggs in one basket, you're sadly mistaken. They're out there somewhere!" (Star Trek: The Magazine Volume 1, Issue 17, p. 18)

Combs relished the fact he was able to play different sides of his character, later stating, "I remember having a conversation with Ira about how I always fantasized that Weyoun would see the error of his ways and go over to the other side, but Ira's point was that the bad guys are the bad guys. Then we had 'Treachery, Faith and the Great River', which was great; that was about the closest we got to the notion of Weyoun crossing over. I liked that Weyoun." (Star Trek: The Magazine Volume 1, Issue 17, p. 18)

Having played several aliens in the Star Trek franchise involving heavy makeup, Combs contrasted his Weyoun makeup with that of a Ferengi; "Weyoun was quite comfortable. It was a longer makeup, even though it looks simpler, because hair was involved; I'd get to a particular place in the makeup and then go get the hair done, and then go back and get finished off. And I could hear quite well, because the ears were little holes." (Star Trek: The Magazine Volume 1, Issue 17, p. 19)

Weyoun's distinctive violet/purple eyes were created by the use of elaborate contact lenses. [3]

Weyoun 5 played a major role in the Deep Space Nine book trilogy Millennium. Shortly after a second, red wormhole destroyed Deep Space 9 in 2374, Weyoun led a fleet of Dominion ships to find out if the new wormhole could go to the Gamma Quadrant after the original blue one would not open. Pursued by Captain Jean-Luc Picard and the USS Enterprise-E, Weyoun and the Dominion ships entered the wormhole, which would not open for the Enterprise, and arrived at a point deep in the Beta Quadrant near the border with the Delta Quadrant. When Weyoun returned to the Alpha Quadrant though the wormhole, he commanded a fleet from an alien race called the Grigari, the Dominion fleet he had taken with him having been destroyed. Weyoun claimed that the "True Prophets" – a group of Prophets inhabiting the red wormhole, from whom the blue wormhole prophets had broken away millennia ago – had anointed him as their kai.

Weyoun's first act was to take the Grigari fleet to Cardassia Prime and try to convince Damar and the Female Changeling to join with the Grigari. When the Female Changeling refused, the Grigari fleet laid waste to the entire Cardassian Union, killing billions, including Damar and the Changeling, effectively ending the Dominion War. Having come to believe that the "True Prophets" were gods, Weyoun went to Vorta and opened the tank containing the next Weyoun to see if anything had been changed in his physiology, only to find that, although there were virtually no differences, Weyoun 6 did not believe in the "True Prophets" as Weyoun 5 believed in them. Weyoun 5 then killed his other clones, and, along with the Grigari, went on to destroy Earth, most of the Human colonies in the Federation, and the Klingon Empire in what became known as the War of the Prophets (β). With powers granted to him by the "True Prophets", along with Grigari nanotechnology, Weyoun was all but unstoppable and immortal. The only real threat to him was the Emissary of the Pah-wraiths, Gul Dukat, who was still possessed by the Kosst AmojanPah-wraith seen in the episode "Tears of the Prophets", and had taken up residence in the mirror universe on Terok Nor.

Weyoun's destructive plans culminated in 2399 when he brought about the end to the entire universe – what he called "pain of life" – with the merging of the blue and red wormholes. The end of the universe, and the timeline, was ultimately avoided after-the-fact by the intervention of two time-traveling groups. The first group was the command staff of DS9, Quark, and Vash who had traveled twenty-five years into the future during the destruction of DS9 in 2374 by the red wormhole. The second was Jean-Luc Picard and Nog, who along with Vash, traveled back right before the end of the universe to the founding of B'hala to set into motion the sequence of events that lead to the opening of the red wormhole in the first place. The first group, without Vash, then managed to restore the station and close the red wormhole in 2374 by traveling back from after the end of the universe to the day when DS9 was destroyed and triggering a collision between Weyoun's ship and a Cardassian ship after the red wormhole opened, killing Weyoun and Dukat, which then pushed a version of the station out of the blue wormhole.

A ninth clone of Weyoun appears in the final book of the Deep Space Nine: Mission Gamma relaunch series. Like Weyoun 4, he is the commander of a Jem'Hadar attack ship, created from the genetic profile left behind in the Gamma Quadrant. Exactly when this clone was activated is not revealed, though it is assumed he was created after the end of the Dominion War. He later becomes Odo's chief aide whenever he is separated from the Great Link.

Weyoun 9 reappears in Olympus Descending, the Dominion entry in the Worlds of Star Trek: Deep Space Nine series. There, it is revealed that Odo specifically reactivated Weyoun so that he would have a familiar face to interact with in the Dominion, and that he is attempting to train the new clone to think for himself rather than blindly follow orders. Weyoun 9 also continues to collect meaningless trinkets in his quarters, just as Weyoun 5 did. Weyoun later appears in the Star Trek: Typhon Pact novel Raise the Dawn.